Microbial 'omics

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# anvi-cluster-contigs [program]

A program to cluster items in a merged anvi'o profile using automatic binning algorithms.

See program help menu or go back to the main page of anvi’o programs and artifacts.

## Usage

This program clusters the contigs stored in a profile-db using your binning algorithm of choice and stores the results in several bins.

This is a quick alternative to manually binning your contigs, but it might miss some details that a human doing manual binning would find. After running this, you might want to run anvi-summarize on the resulting collection to look through your bins, and, if necessary, use anvi-refine to change the contents of them.

You have to option to use several different clustering algorithms, which you’ll specify with the driver parameter: concoct, metabat2, maxbin2, dastool, and binsanity.

So, a run of this program will look like the following:

anvi-cluster-contigs -p profile-db \ -c contigs-db \ -C collection \ --driver concoct

Once you specify an algorithm, there are many algorithm specific parameters that you can change to your liking. When this program is set up, these parameters will appear in the help menu for the algorithms that anvi’o can find.

Edit this file to update this information.

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.